Updated: Wed May 31 01:52:16 2017

RPKM of DNA methylation regulators

CpG coverage profile

  • TCGA data have particularly lower coverage.

Global hypermethylation in IDH mut glioma

  • Genome-wide and CGI hypermethylation in IDH mutant glioma samples: CEMT19, CEMT22, and CEMT_47.
  • CEMT_21 (10% IDH mutation frequency) showed methylation levels closer to IDH wildtype samples.
  • TCGA data seem to have lower fractional methylation geonme-wide, possibly due to different processing pipeline.
  • Whiskers of the box plot represent 10% and 90% quantile.

Clustering

  • CGI clustering showed clusters based on IDH mut and wt.

Enhancer and 5mC

  • Hypermethylated enhancers also present at promoters - more so in IDH mutant glioma
  • Expression levels of the closest genes are not significantly affected by 5mC at these bivalent enhancers
  • Genes associated with each profile group are significantly overlapped across the three IDH mutant gliomas

DNA methylation changes around CGI edges

  • CGIs are hypermethylated in IDH mutant gliomas.
  • DNA methylation changes around CGI occur at the edge of CGIs.

DMRs between gliomas and NPCs

DMR identification

  • Identify DM CpGs
    • CpG coverage in both samples \(\ge\) 3;
    • methyl_diff one-sided p-value \(\le\) 0.0005;
    • delta fractional methylation \(\ge\) 0.6;
    • fractional methylation of one sample \(\ge\) 0.75.
  • Collapse DM CpGs into DMRs
    • adjacent DM CpGs have the same DM status;
    • distance between adjacent CpGs (size) \(\le\) 500bp;
    • No. of CpGs within each DMR \(\ge\) 3.

Total DMR length

  • Hypermethylation in IDH mut samples.
  • Hypomethylation in IDH wt glioma: CEMT_23 (GBM).
  • CEMT_21 had the least amount of DMRs and no bias towards hyper or hypo.
  • Results against different NPCs were reasonably similar (intersect statistically significant).

DMR GREAT analysis

  • DMR - gene association
    • Proximal: 5kb upstream, 1kb downstream.
    • Distal: up to 20kb.

Hypermethylated DMRs

  • IDH mut and wt samples showed different terms, and CEMT_21 showed similar terms as wt.
    • Disease Ontology: mut showed CNS/brain disease.
    • GOBP: mut showed neurogenesis/brain development, wt showed regulation of biosynthetic process.
    • GOCC: wt showed transcription factor complex, mut also showed membranes and neurons.

Hypomethylated DMRs

  • IDH mut had few significant term (CEMT22 had none), wt had cancer related terms, and CEMT21 showed similar terms to mut.

Percentage of hyper CpGs in hyper CGIs

Methylated CGIs associated with transcription

Sample CGI CGI_hyper CGI_K36 CGI_hyper_K36 p
CEMT_19 5066 1685 290 216 0
CEMT_21 5066 1085 126 91 0
CEMT_22 5066 1739 328 227 0
CEMT_23 5066 1015 218 103 0
CEMT_47 5066 1724 165 138 0

Hypermethylated CGIs associated with transcription

  • There are on average 15% of hypermethylated CGIs overlapping with H3K36me3 enriched regions, 8% of them are not in genebody in IDH mut gliomas, suggesting possible enhancer RNA expression.
Sample hyper CGI Non.gene_CGI H3K36me3 Non.gene p_Fisher
CEMT_19 19105 6042 1197 946 72 1.0000000
CEMT_21 1793 313 50 61 5 0.9568727
CEMT_22 17291 4733 919 843 64 1.0000000
CEMT_23 1718 703 107 162 5 1.0000000
CEMT_47 22146 6034 1222 629 36 1.0000000
DMR_CGI_K36

DMR_CGI_K36

DMR enrichment in genomic regions

  • Enriched in CGIs and CGI shores, esp. hypermethylation in CGIs.
  • Promoter: TSS +/- 2kb; CGI_shore: CGI +/- 2kb.

DMR enrichment in chromatin states

  • Hypermethylated regions were enriched in H3K27me3 marked chromatin states.
  • Hypomethylated regions were enriched in enhancer regions.

DMR intersect with differentially marked histone modifications

DMR associated with DE genes

  • Hypermethylated DMRs in the promoter regions are significantly associated with both UP and DN regulated genes.
Sample hyper_promoter UP_2FC H3K27ac
CEMT_19 7921 1951 1340
CEMT_21 429 86 53
CEMT_22 6830 1675 1053
CEMT_23 640 215 62
CEMT_47 8254 1972 1357

DMR_CGI_UP